wgEncodeGencodeSuper
Description
The aim of the GENCODE
Genes project (Harrow et al., 2006) is to produce a set of
highly accurate annotations of evidence-based gene features on the human reference genome.
This includes the identification of all protein-coding loci with associated
alternative splice variants, non-coding with transcript evidence in the public
databases (NCBI/EMBL/DDBJ) and pseudogenes. A high quality set of gene
structures is necessary for many research studies such as comparative or
evolutionary analyses, or for experimental design and interpretation of the
results.
The GENCODE Genes tracks display the high-quality manual annotations merged
with evidence-based automated annotations across the entire
human genome. The GENCODE gene set presents a full merge
between HAVANA manual annotation and Ensembl automatic annotation.
Priority is given to the manually curated HAVANA annotation using predicted
Ensembl annotations when there are no corresponding manual annotations. With
each release, there is an increase in the number of annotations that have undergone
manual curation.
This annotation was carried out on the GRCm38 (mm10) genome assembly.
Experimental verification details are given in each descriptions for each
track.
Display Conventions
These are multi-view composite tracks that contain differing data sets
(views). Instructions for configuring multi-view tracks are
here.
Only some subtracks are shown by default. The user can select which subtracks
are displayed via the display controls on the track details pages.
Further details on display conventions and data interpretation are available in the track descriptions.
Release Notes
See also: The GENCODE Project Release History.
Credits
This GENCODE release is the result of a collaborative effort among
the following laboratories: (contact:
GENCODE at the Sanger Institute)
| Lab/Institution |
Contributors |
| GENCODE Principal Investigator |
Tim Hubbard |
| HAVANA manual annotation group, Wellcome Trust Sanger Insitute (WTSI), Hinxton, UK |
Jennifer Harrow, Stephen Searle, Timothy Cutts, Bronwen Aken, James Gilbert, Jyoti Choudhary, Ed Griffiths, Ewan Birney, Jose Manuel Gonzalez, Electra Tapanari, Daniel Barrell, Adam Frankish, Andrew Berry, Alexandra Bignell, Veronika Boychenko, Claire Davidson, Gloria Despacio-Reyes, Mike Kay, Deepa Manthravadi, Gaurab Mukherjee, Catherine Snow, Gemma Barson, Matt Hardy, Joanne Howes |
| Centre de Regulació Genòmica (CRG), Barcelona, Spain |
Roderic Guigó, Julien Lagarde, Barbara Uszczy𑀪ska |
| Genome Bioinformatics, University of California Santa Cruz (UCSC), USA |
David Haussler, Rachel Harte, Mark Diekhans, Benedict Paten, Joel Armstrong |
| Computer Science and Artificial Intelligence Lab,Broad Institute of MIT and Harvard, USA |
Manolis Kellis, Irwin Jungreis |
| Computational Biology and Bioinformatics, Yale University (Yale), USA |
Mark Gerstein, Suganthi Balasubramanian, Ekta Khurana, Cristina Sisu, Baikang Pei, Yan Zhang, Mihali Felipe |
| Center for Integrative Genomics,University of Lausanne, Switzerland |
Alexandre Reymond, Cedric Howald, Anne-Maud Ferreira, Jacqueline Chrast |
| Structural Computational Biology Group, Centro Nacional de Investigaciones Oncologicas (CNIO), Madrid, Spain |
Alfonso Valencia, Michael Tress, José Manuel Rodríguez, Victor de la Torre |
| Former members of the GENCODE project |
Felix Kokocinski, Toby Hunt, Gary Saunders, Sarah Grubb, Thomas Derrien, Andrea Tanzer, Gang Fang, Mihali Felipe, Michael Brent, Randall Brown, Jeltje van Baren |
Contact:
GENCODE at the Sanger Institute
References
Coffey AJ, Kokocinski F, Calafato MS, Scott CE, Palta P, Drury E, Joyce CJ, Leproust EM, Harrow J,
Hunt S et al.
The GENCODE exome: sequencing the complete human exome.
Eur J Hum Genet. 2011 Jul;19(7):827-31.
PMID: 21364695; PMC: PMC3137498
Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S,
Fitzgerald S et al.
Ensembl 2012.
Nucleic Acids Res. 2012 Jan;40(Database issue):D84-90.
PMID: 22086963; PMC: PMC3245178
Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R,
Swarbreck D et al.
GENCODE: producing a reference annotation for ENCODE.
Genome Biol. 2006;7 Suppl 1:S4.1-9.
PMID: 16925838; PMC: PMC1810553
Publications
Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM, Howald C, Foissac S, Ucla C, Chrast
J et al.
Evidence for transcript networks composed of chimeric RNAs in human cells.
PLoS One. 2012;7(1):e28213.
PMID: 22238572; PMC: PMC3251577
Ezkurdia I, del Pozo A, Frankish A, Rodriguez JM, Harrow J, Ashman K, Valencia A, Tress ML.
Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved
structure and function.
Mol Biol Evol. 2012 Sep;29(9):2265-83.
PMID: 22446687; PMC: PMC3424414
Publications link for the GENCODE project
Data Release Policy
GENCODE data are available for use without restrictions.
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